feat(sync): re-resolve affected files incrementally

[Alvin-ne]

Summary

• add persisted reference_facts to keep extracted references available for future incremental re-resolution
• mark resolver-generated edges with provenance: 'resolver'
• extend sync() to re-resolve affected files, not just directly changed files
• surface sync mode details in CLI and MCP status output

Details

• add schema v5 migration for reference_facts
• clear and rebuild resolver/heuristic edges by file during incremental sync
• re-run heuristic callback synthesis after incremental resolve
• add sync test coverage for affected-file re-resolution

Validation

• npm run build
• CODEGRAPH_ALLOW_UNSAFE_NODE=1 npm test -- __tests__/sync.test.ts
• CODEGRAPH_ALLOW_UNSAFE_NODE=1 npm test -- __tests__/integration/full-pipeline.test.ts
• CODEGRAPH_ALLOW_UNSAFE_NODE=1 npm test -- __tests__/frameworks-integration.test.ts
• CODEGRAPH_ALLOW_UNSAFE_NODE=1 npm test -- __tests__/mcp-staleness-banner.test.ts